title: Evolutionary principles of modular gene regulation in yeasts.
abstract: Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years [corrected]. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles. DOI:http://dx.doi.org/10.7554/eLife.00603.001.
authors.affiliation: Broad Institute of MIT and Harvard , Cambridge , United States.
authors.forename: Dawn A
authors.initials: DA
authors.lastname: Thompson
authors.forename: Sushmita
authors.initials: S
authors.lastname: Roy
authors.forename: Michelle
authors.initials: M
authors.lastname: Chan
authors.forename: Mark P
authors.initials: MP
authors.lastname: Styczynsky
authors.forename: Jenna
authors.initials: J
authors.lastname: Pfiffner
authors.forename: Courtney
authors.initials: C
authors.lastname: French
authors.forename: Amanda
authors.initials: A
authors.lastname: Socha
authors.forename: Anne
authors.initials: A
authors.lastname: Thielke
authors.forename: Sara
authors.initials: S
authors.lastname: Napolitano
authors.forename: Paul
authors.initials: P
authors.lastname: Muller
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Jay H
authors.initials: JH
authors.lastname: Konieczka
authors.forename: Ilan
authors.initials: I
authors.lastname: Wapinski
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D010802:Phylogeny; D014158:Transcription, Genetic
keywords: S. cerevisiae; S. pombe; carbon lifestyle; divergence; duplication; gene expression; module; regulatory evolution